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ehmmbuild |
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Usage:
ehmmbuild [options] alignfile hmmfile
Important note: the alignfile (input) and hmmfile (output) parameters are specified in the reverse order in the original HMMER.
hmmbuild reads a multiple sequence alignment file
% ehmmbuild globins50.msf globin.hmm -nhmm globins50 -strategy D Build a profile HMM from an alignment. hmmbuild - build a hidden Markov model from an alignment HMMER 2.3.2 (Oct 2003) Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment file: ../../data/hmmnew/globins50.msf File format: MSF Search algorithm configuration: Multiple domain (hmmls) Model construction strategy: MAP (gapmax hint: 0.50) Null model used: (default) Prior used: (default) Sequence weighting method: G/S/C tree weights New HMM file: globin.hmm [appending] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment: #1 Number of sequences: 50 Number of columns: 308 Determining effective sequence number ... done. [2] Weighting sequences heuristically ... done. Constructing model architecture ... done. Converting counts to probabilities ... done. Setting model name, etc. ... done. [globins50] Constructed a profile HMM (length 143) Average score: 189.04 bits Minimum score: -17.62 bits Maximum score: 234.09 bits Std. deviation: 53.18 bits Finalizing model configuration ... done. Saving model to file ... done. // /shared/software/bin/hmmbuild -n globins50 --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F globin.hmm ../../data/hmmnew/globins50.msf |
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Example 2
% ehmmbuild rrm.sto myhmms -nhmm rrm -strategy D Build a profile HMM from an alignment. hmmbuild - build a hidden Markov model from an alignment HMMER 2.3.2 (Oct 2003) Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment file: ../../data/hmmnew/rrm.sto File format: Stockholm Search algorithm configuration: Multiple domain (hmmls) Model construction strategy: MAP (gapmax hint: 0.50) Null model used: (default) Prior used: (default) Sequence weighting method: G/S/C tree weights New HMM file: myhmms [appending] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment: #1 Number of sequences: 90 Number of columns: 104 Determining effective sequence number ... done. [88] Weighting sequences heuristically ... done. Constructing model architecture ... done. Converting counts to probabilities ... done. Setting model name, etc. ... done. [rrm] Constructed a profile HMM (length 77) Average score: 75.37 bits Minimum score: 26.86 bits Maximum score: 119.83 bits Std. deviation: 21.78 bits Finalizing model configuration ... done. Saving model to file ... done. // /shared/software/bin/hmmbuild -n rrm --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../data/hmmnew/rrm.sto |
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Example 3
% ehmmbuild fn3.sto myhmms -nhmm fn3 -strategy D Build a profile HMM from an alignment. hmmbuild - build a hidden Markov model from an alignment HMMER 2.3.2 (Oct 2003) Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment file: ../../data/hmmnew/fn3.sto File format: Stockholm Search algorithm configuration: Multiple domain (hmmls) Model construction strategy: MAP (gapmax hint: 0.50) Null model used: (default) Prior used: (default) Sequence weighting method: G/S/C tree weights New HMM file: myhmms [appending] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment: fn3 Number of sequences: 108 Number of columns: 119 Determining effective sequence number ... done. [108] Weighting sequences heuristically ... done. Constructing model architecture ... done. Converting counts to probabilities ... done. Setting model name, etc. ... done. [fn3] Constructed a profile HMM (length 84) Average score: 67.54 bits Minimum score: 27.53 bits Maximum score: 105.77 bits Std. deviation: 17.07 bits Finalizing model configuration ... done. Saving model to file ... done. // /shared/software/bin/hmmbuild -n fn3 --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../data/hmmnew/fn3.sto |
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Example 4
% ehmmbuild pkinase.sto myhmms -nhmm pkinase -strategy D Build a profile HMM from an alignment. hmmbuild - build a hidden Markov model from an alignment HMMER 2.3.2 (Oct 2003) Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment file: ../../data/hmmnew/pkinase.sto File format: Stockholm Search algorithm configuration: Multiple domain (hmmls) Model construction strategy: MAP (gapmax hint: 0.50) Null model used: (default) Prior used: (default) Sequence weighting method: G/S/C tree weights New HMM file: myhmms [appending] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment: pkinase Number of sequences: 67 Number of columns: 471 Determining effective sequence number ... done. [67] Weighting sequences heuristically ... done. Constructing model architecture ... done. Converting counts to probabilities ... done. Setting model name, etc. ... done. [pkinase] Constructed a profile HMM (length 294) Average score: 312.79 bits Minimum score: 176.48 bits Maximum score: 390.44 bits Std. deviation: 44.60 bits Finalizing model configuration ... done. Saving model to file ... done. // /shared/software/bin/hmmbuild -n pkinase --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../data/hmmnew/pkinase.sto |
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More or less all options documented as "expert" in the original hmmer user guide are given in ACD as "advanced" options (-options must be specified on the command-line in order to be prompted for a value for them).
Build a profile HMM from an alignment. Version: EMBOSS:6.2.0 Standard (Mandatory) qualifiers: [-alignfile] seqset (Aligned) protein sequence set filename and optional format, or reference (input USA) -nhmm string Name for this HMM. The name can be any string of non-whitespace characters (e.g. one 'word'). There is no length limit (at least not one imposed by HMMER; your shell will complain about command line lengths frst). (Any word) -strategy menu [D] All alignments are local with respect to the sequence and are configured to be local (fragmentary) or global with respect to the HMM. The model is also configured to find a single or multiple domains (matches) to a sequence. The options for configuring the model are as follows: (D): The default setting. Multiple domains per sequence, global alignments with respect to the HMM. (F): Multiple domains per sequence, local alignments with respect to the HMM. Analogous to the old hmmfs program of HMMER 1. (G) Single domain per sequence, global alignment with respect to the HMM. Analogous to the old hmms program of HMMER 1. (S) Single domain per sequence, local alignments with respect to the HMM. Analogous to the old hmmsw program of HMMER 1. (Values: D (global-multidomain); F (local-multidomain); G (global-singledomain); S (local-singledomain)) [-hmmfile] outfile [*.ehmmbuild] HMMER hidden markov model output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -prior infile Read a Dirichlet prior from file, replacing the default mixture Dirichlet. The format of prior files is documented in the User's Guide, and an example is given in the Demos directory of the HMMER distribution. -null infile Read a null model from file. The default for protein is to use average amino acid frequencies from Swissprot 34 and p1 = 350/351; for nucleic acid, the default is to use 0.25 for each base and p1 = 1000/1001. For documentation of the format of the null model file and further explanation of how the null model is used, see the User's Guide. -pam infile Apply a heuristic PAM- (substitution matrix-) based prior on match emission probabilities instead of the default mixture Dirichlet. The substitution matrix is read from file. See -pamwgt. The default Dirichlet state transition prior and insert emission prior are unaffected. Therefore in principle you could combine -prior with -pam but this isn't recommended, as it hasn't been tested. ( -pam itself hasn't been tested much!) -pamwgt float [20.0] Controls the weight |
Qualifier | Type | Description | Allowed values | Default | ||||||||||||
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Standard (Mandatory) qualifiers | ||||||||||||||||
[-alignfile] (Parameter 1) |
seqset | (Aligned) protein sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required | ||||||||||||
-nhmm | string | Name for this HMM. The name can be any string of non-whitespace characters (e.g. one 'word'). There is no length limit (at least not one imposed by HMMER; your shell will complain about command line lengths frst). | Any word | |||||||||||||
-strategy | list | All alignments are local with respect to the sequence and are configured to be local (fragmentary) or global with respect to the HMM. The model is also configured to find a single or multiple domains (matches) to a sequence. The options for configuring the model are as follows: (D): The default setting. Multiple domains per sequence, global alignments with respect to the HMM. (F): Multiple domains per sequence, local alignments with respect to the HMM. Analogous to the old hmmfs program of HMMER 1. (G) Single domain per sequence, global alignment with respect to the HMM. Analogous to the old hmms program of HMMER 1. (S) Single domain per sequence, local alignments with respect to the HMM. Analogous to the old hmmsw program of HMMER 1. |
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D | ||||||||||||
[-hmmfile] (Parameter 2) |
outfile | HMMER hidden markov model output file | Output file | <*>.ehmmbuild | ||||||||||||
Additional (Optional) qualifiers | ||||||||||||||||
(none) | ||||||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||||||
-prior | infile | Read a Dirichlet prior from file, replacing the default mixture Dirichlet. The format of prior files is documented in the User's Guide, and an example is given in the Demos directory of the HMMER distribution. | Input file | Required | ||||||||||||
-null | infile | Read a null model from file. The default for protein is to use average amino acid frequencies from Swissprot 34 and p1 = 350/351; for nucleic acid, the default is to use 0.25 for each base and p1 = 1000/1001. For documentation of the format of the null model file and further explanation of how the null model is used, see the User's Guide. | Input file | Required | ||||||||||||
-pam | infile | Apply a heuristic PAM- (substitution matrix-) based prior on match emission probabilities instead of the default mixture Dirichlet. The substitution matrix is read from file. See -pamwgt. The default Dirichlet state transition prior and insert emission prior are unaffected. Therefore in principle you could combine -prior with -pam but this isn't recommended, as it hasn't been tested. ( -pam itself hasn't been tested much!) | Input file | Required | ||||||||||||
-pamwgt | float | Controls the weight <x> on a PAM-based prior. Only has effect if -pam option is also in use. <x> is a positive real number, 20.0 by default. <x> is the number of 'pseudocounts' contriubuted by the heuristic prior. Very high values of <x> can force a scoring system that is entirely driven by the substitution matrix, making HMMER somewhat approximate Gribskov profiles. | Any numeric value | 20.0 | ||||||||||||
-pbswitch | integer | For alignments with a very large number of sequences, the GSC, BLOSUM, and Voronoi weighting schemes are slow; they're O(N^2) for N sequences. Henikoff position-based weights (PB weights) are more effcient. At or above a certain threshold sequence number <n> hmmbuild will switch from GSC, BLOSUM, or Voronoi weights to PB weights. To disable this switching behavior (at the cost of compute time, set <n> to be something larger than the number of sequences in your alignment. <n> is a positive integer; the default is 1000. | Any integer value | 1000 | ||||||||||||
-archpri | float | The value of the 'architecture prior' used by MAP architecture construction. This value is a probability between 0 and 1. This parameter governs a geometric prior distribution over model lengths. As 'archpri' increases, longer models are favored a priori. As 'archpri' decreases, it takes more residue conservation in a column to make a column a 'consensus' match column in the model architecture. The 0.85 default has been chosen empirically as a reasonable setting. | Any numeric value | 0.85 | ||||||||||||
-binary | boolean | Write the HMM to file in HMMER binary format instead of readable ASCII text. | Boolean value Yes/No | No | ||||||||||||
-fast | boolean | Quickly and heuristically determine the architecture of the model by assigning all columns with more than a certain fraction of gap characters to insert states. By default this fraction is 0.5, and it can be changed using the --gapmax option. The default construction algorithm is a maximum a posteriori (MAP) algorithm, which is slower. | Boolean value Yes/No | No | ||||||||||||
-gapmax | float | Controls the -fast model construction algorithm, but if -fast is not being used, has no effect. If a column has more than a fraction <x> of gap symbols in it, it gets assigned to an insert column. <x> is a frequency from 0 to 1, and by default is set to 0.5. Higher values of <x> mean more columns get assigned to consensus, and models get longer; smaller values of <x> mean fewer columns get assigned to consensus, and models get smaller. | Any numeric value | 0.5 | ||||||||||||
-hand | boolean | Specify the architecture of the model by hand: the alignment file must be in SELEX or Stockholm format, and the reference annotation line (RF in SELEX, GC RF in Stockholm) is used to specify the architecture. Any column marked with a non-gap symbol (such as an 'x', for instance) is assigned as a consensus (match) column in the model. | Boolean value Yes/No | No | ||||||||||||
-sidlevel | float | Controls both the determination of effective sequence number and the behavior of the -wblosum weighting option. The sequence alignment is clustered by percent identity, and the number of clusters at a cutoff threshold of <x> is used to determine the effective sequence number. Higher values of <x> give more clusters and higher effective sequence numbers; lower values of <x> give fewer clusters and lower effective sequence numbers. <x> is a fraction from 0 to 1, and by default is set to 0.62 (corresponding to the clustering level used in constructing the BLOSUM62 substitution matrix). | Any numeric value | 0.62 | ||||||||||||
-noeff | boolean | Turn off the effective sequence number calculation, and use the true number of sequences instead. This will usually reduce the sensitivity of the final model (so don't do it without good reason!) | Boolean value Yes/No | No | ||||||||||||
-swentry | float | Controls the total probability that is distributed to local entries into the model, versus starting at the beginning of the model as in a global alignment. <x> is a probability from 0 to 1, and by default is set to 0.5. Higher values of <x> mean that hits that are fragments on their left (N or 5'-terminal) side will be penalized less, but complete global alignments will be penalized more. Lower values of <x> mean that fragments on the left will be penalized more, and global alignments on this side will be favored. This option only affects the confgurations that allow local alignments, e.g. -s and -f; unless one of these options is also activated, this option has no effect. You have independent control over local/global alignment behavior for the N/C (5'/3') termini of your target sequences using --swentry and --swexit. | Any numeric value | 0.5 | ||||||||||||
-swexit | float | Controls the total probability that is distributed to local exits from the model, versus ending an alignment at the end of the model as in a global alignment. <x> is a probability from 0 to 1, and by default is set to 0.5. Higher values of <x> mean that hits that are fragments on their right (C or 3'-terminal) side will be penalized less, but complete global alignments will be penalized more. Lower values of <x> mean that fragments on the right will be penalized more, and global alignments on this side will be favored. This option only affects the confgurations that allow local alignments, e.g. -s and -f; unless one of these options is also activated, this option has no effect. You have independent control over local/global alignment behavior for the N/C (5'/3') termini of your target sequences using -swentry and -swexit. | Any numeric value | 0.5 | ||||||||||||
-verbosity | boolean | Print more possibly useful stuff, such as the individual scores for each sequence in the alignment. | Boolean value Yes/No | No | ||||||||||||
-weighting | list | Values (B)(-wblosum in HMMER) Use the BLOSUM filtering algorithm to weight the sequences. Cluster the sequences at a given percentage identity (see -idlevel); assign each cluster a total weight of 1.0, distributed equally amongst the members of that cluster. (G)(-wgsc in HMMER) Use the Gerstein/Sonnhammer/Chothia ad hoc sequence weighting algorithm. This is the default. (K)(-wme in HMMER) Use the Krogh/Mitchison maximum entropy algorithm to 'weight' the sequences. This supercedes the Eddy/Mitchison/Durbin maximum discrimination algorithm, which gives almost identical weights but is less robust. ME weighting seems to give a marginal increase in sensitivity over the default GSC weights, but takes a fair amount of time. (W) (-wpb in HMMER) Use the Henikoff position-based weighting scheme. (V) (-wvoronoi in HMMER) Use the Sibbald/Argos Voronoi sequence weighting algorithm in place of the default GSC weighting. (N) (-wnone in HMMER) Turn off all sequence weighting. |
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G | ||||||||||||
-o | outfile | Re-save the starting alignment to file, in Stockholm format. The columns which were assigned to match states will be marked with x's in an RF annotation line. If either the -hand or -fast construction options were chosen, the alignment may have been slightly altered to be compatible with Plan 7 transitions, so saving the final alignment and comparing to the starting alignment can let you view these alterations. See the User's Guide for more information on this arcane side effect. | Output file | <*>.ehmmbuild | ||||||||||||
-cfile | outfile | Save the observed emission and transition counts to file after the architecture has been determined (e.g. after residues/gaps have been assigned to match, delete, and insert states). This option is used in HMMER development for generating data files useful for training new Dirichlet priors. The format of count files is documented in the User's Guide. | Output file | <*>.ehmmbuild | ||||||||||||
Associated qualifiers | ||||||||||||||||
"-alignfile" associated seqset qualifiers | ||||||||||||||||
-sbegin1 -sbegin_alignfile |
integer | Start of each sequence to be used | Any integer value | 0 | ||||||||||||
-send1 -send_alignfile |
integer | End of each sequence to be used | Any integer value | 0 | ||||||||||||
-sreverse1 -sreverse_alignfile |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||||||||
-sask1 -sask_alignfile |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||||||||
-snucleotide1 -snucleotide_alignfile |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||||||||
-sprotein1 -sprotein_alignfile |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||||||||
-slower1 -slower_alignfile |
boolean | Make lower case | Boolean value Yes/No | N | ||||||||||||
-supper1 -supper_alignfile |
boolean | Make upper case | Boolean value Yes/No | N | ||||||||||||
-sformat1 -sformat_alignfile |
string | Input sequence format | Any string | |||||||||||||
-sdbname1 -sdbname_alignfile |
string | Database name | Any string | |||||||||||||
-sid1 -sid_alignfile |
string | Entryname | Any string | |||||||||||||
-ufo1 -ufo_alignfile |
string | UFO features | Any string | |||||||||||||
-fformat1 -fformat_alignfile |
string | Features format | Any string | |||||||||||||
-fopenfile1 -fopenfile_alignfile |
string | Features file name | Any string | |||||||||||||
"-hmmfile" associated outfile qualifiers | ||||||||||||||||
-odirectory2 -odirectory_hmmfile |
string | Output directory | Any string | |||||||||||||
"-o" associated outfile qualifiers | ||||||||||||||||
-odirectory | string | Output directory | Any string | |||||||||||||
"-cfile" associated outfile qualifiers | ||||||||||||||||
-odirectory | string | Output directory | Any string | |||||||||||||
General qualifiers | ||||||||||||||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||||||||
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||||||||
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||||||||
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||||||||
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||||||||
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||||||||
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||||||||
-warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||||||||
-error | boolean | Report errors | Boolean value Yes/No | Y | ||||||||||||
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||||||||
-die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||||||||
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
ehmmbuild reads any normal sequence USAs.
!!AA_MULTIPLE_ALIGNMENT 1.0 PileUp of: *.pep Symbol comparison table: GenRunData:blosum62.cmp CompCheck: 6430 GapWeight: 12 GapLengthWeight: 4 pileup.msf MSF: 308 Type: P August 16, 1999 09:09 Check: 9858 .. Name: lgb1_pea Len: 308 Check: 2200 Weight: 1.00 Name: lgb1_vicfa Len: 308 Check: 214 Weight: 1.00 Name: myg_escgi Len: 308 Check: 3961 Weight: 1.00 Name: myg_horse Len: 308 Check: 5619 Weight: 1.00 Name: myg_progu Len: 308 Check: 6401 Weight: 1.00 Name: myg_saisc Len: 308 Check: 6606 Weight: 1.00 Name: myg_lycpi Len: 308 Check: 6090 Weight: 1.00 Name: myg_mouse Len: 308 Check: 6613 Weight: 1.00 Name: myg_musan Len: 308 Check: 3942 Weight: 1.00 Name: hba_ailme Len: 308 Check: 4558 Weight: 1.00 Name: hba_prolo Len: 308 Check: 5054 Weight: 1.00 Name: hba_pagla Len: 308 Check: 5383 Weight: 1.00 Name: hba_macfa Len: 308 Check: 5135 Weight: 1.00 Name: hba_macsi Len: 308 Check: 5198 Weight: 1.00 Name: hba_ponpy Len: 308 Check: 5050 Weight: 1.00 Name: hba2_galcr Len: 308 Check: 5609 Weight: 1.00 Name: hba_mesau Len: 308 Check: 4702 Weight: 1.00 Name: hba2_bosmu Len: 308 Check: 4241 Weight: 1.00 Name: hba_erieu Len: 308 Check: 4680 Weight: 1.00 Name: hba_frapo Len: 308 Check: 3549 Weight: 1.00 Name: hba_phaco Len: 308 Check: 4440 Weight: 1.00 Name: hba_trioc Len: 308 Check: 5465 Weight: 1.00 Name: hba_ansse Len: 308 Check: 3300 Weight: 1.00 Name: hba_colli Len: 308 Check: 3816 Weight: 1.00 Name: hbad_chlme Len: 308 Check: 4571 Weight: 1.00 Name: hbad_pasmo Len: 308 Check: 6777 Weight: 1.00 Name: hbaz_horse Len: 308 Check: 7187 Weight: 1.00 Name: hba4_salir Len: 308 Check: 7329 Weight: 1.00 Name: hbb_ornan Len: 308 Check: 2667 Weight: 1.00 Name: hbb_tacac Len: 308 Check: 4356 Weight: 1.00 Name: hbe_ponpy Len: 308 Check: 3827 Weight: 1.00 Name: hbb_speci Len: 308 Check: 1556 Weight: 1.00 Name: hbb_speto Len: 308 Check: 2051 Weight: 1.00 Name: hbb_equhe Len: 308 Check: 3414 Weight: 1.00 Name: hbb_sunmu Len: 308 Check: 2927 Weight: 1.00 Name: hbb_calar Len: 308 Check: 3836 Weight: 1.00 Name: hbb_mansp Len: 308 Check: 4322 Weight: 1.00 Name: hbb_ursma Len: 308 Check: 4428 Weight: 1.00 Name: hbb_rabit Len: 308 Check: 4190 Weight: 1.00 Name: hbb_tupgl Len: 308 Check: 4185 Weight: 1.00 [Part of this file has been deleted for brevity] lgb1_pea ~~~~~~~~ lgb1_vicfa ~~~~~~~~ myg_escgi ~~~~~~~~ myg_horse ~~~~~~~~ myg_progu ~~~~~~~~ myg_saisc ~~~~~~~~ myg_lycpi ~~~~~~~~ myg_mouse ~~~~~~~~ myg_musan ~~~~~~~~ hba_ailme ~~~~~~~~ hba_prolo ~~~~~~~~ hba_pagla ~~~~~~~~ hba_macfa ~~~~~~~~ hba_macsi ~~~~~~~~ hba_ponpy ~~~~~~~~ hba2_galcr ~~~~~~~~ hba_mesau ~~~~~~~~ hba2_bosmu ~~~~~~~~ hba_erieu ~~~~~~~~ hba_frapo ~~~~~~~~ hba_phaco ~~~~~~~~ hba_trioc ~~~~~~~~ hba_ansse ~~~~~~~~ hba_colli ~~~~~~~~ hbad_chlme ~~~~~~~~ hbad_pasmo ~~~~~~~~ hbaz_horse ~~~~~~~~ hba4_salir ~~~~~~~~ hbb_ornan ~~~~~~~~ hbb_tacac ~~~~~~~~ hbe_ponpy ~~~~~~~~ hbb_speci ~~~~~~~~ hbb_speto ~~~~~~~~ hbb_equhe ~~~~~~~~ hbb_sunmu ~~~~~~~~ hbb_calar ~~~~~~~~ hbb_mansp ~~~~~~~~ hbb_ursma ~~~~~~~~ hbb_rabit ~~~~~~~~ hbb_tupgl ~~~~~~~~ hbb_triin ~~~~~~~~ hbb_colli ~~~~~~~~ hbb_larri ~~~~~~~~ hbb1_varex ~~~~~~~~ hbb2_xentr ~~~~~~~~ hbbl_ranca ~~~~~~~~ hbb2_tricr ~~~~~~~~ glb2_mormr ~~~~~~~~ glbz_chith FGAVFAKM hbf1_ureca VAAMK~~~ |
# STOCKHOLM 1.0 YIS5_YEAST/33-104 IYIGNL......NRELTEGDILTVFS.....E.YGVP..VDVILSRD... YIS1_YEAST/66-136 IFVGNI......TPDVTPEQIEDHFK.....D.CGQI..KRITLLYD... RN15_YEAST/20-91 VYLGSI......PYDQTEEQILDLCS.....N.VGPV..INLKMMFD... CST2_HUMAN/18-89 VFVGNI......PYEATEEQLKDIFS.....E.VGPV..VSFRLVYD... NSR1_YEAST/269-340 LFLGNL......SFNADRDAIFELFA.....K.HGEV..VSVRIPTH... IF4B_HUMAN/98-168 AFLGNL......PYDVTEESIKEFFR.....G.LNIS...AVRLPR.... TIA1_HUMAN/108-179 VFVGDL......SPQITTEDIKAAFA.....P.FGRI..SDARVVKD... PUB1_YEAST/163-234 LFVGDL......NVNVDDETLRNAFK.....D.FPSY..LSGHVMWD... NAM8_YEAST/165-237 IFVGDL......APNVTESQLFELFI.....NRYAST..SHAKIVHD... RT19_ARATH/33-104 LYIGGL......SPGTDEHSLKDAFS.....S.FNGV..TEARVMTN... NSR1_YEAST/170-241 IFVGRL......SWSIDDEWLKKEFE.....H.IGGV..IGARVIYE... PES4_YEAST/93-164 LFIGDL......HETVTEETLKGIFK.....K.YPSF..VSAKVCLD... PABP_DROME/4-75 LYVGDL......PQDVNESGLFDKFS.....S.AGPV..LSIRVCRD... NOP4_YEAST/28-98 LFVRSI......PQDVTDEQLADFFS.....N.FAPI..KHAVVVKD... ROC5_NICSY/219-290 LYVANL......SWALTSQGLRDAFA.....D.QPGF..MSAKVIYD... ROC5_NICSY/116-187 LYVGNL......PFSMTSSQLSEIFA.....E.AGTV..ANVEIVYD... ROC3_NICSY/99-170 LFVGNL......PYDIDSEGLAQLFQ.....Q.AGVV..EIAEVIYN... GBP2_YEAST/221-291 VFIINL......PYSMNWQSLKDMFK.....E.CGHV..LRADVELD... PABP_SCHPO/263-333 VYIKNL......DTEITEQEFSDLFG.....Q.FGEI..TSLSLVKD... PABP_DROME/183-254 VYVKNF......TEDFDDEKLKEFFE.....P.YGKI..TSYKVMS.... PABP_DROME/92-162 VFIKNL......DRAIDNKAIYDTFS.....A.FGNI..LSCKVATD... SFR3_HUMAN/12-78 VYVGNL......GNNGNKTELERAFG.....Y.YGPL..RSVWVARN... SR55_DROME/5-68 VYVGGL......PYGVRERDLERFFK.....G.YGRT..RDILIKN.... SFR1_HUMAN/17-85 IYVGNL......PPDIRTKDIEDVFY.....K.YGAI..RDIDLKNR... SFR2_CHICK/16-87 LKVDNL......TYRTSPDTLRRVFE.....K.YGRV..GDVYIPRD... ROG_HUMAN/10-81 LFIGGL......NTETNEKALEAVFG.....K.YGRI..VEVLLMKD... TRA2_DROME/99-170 IGVFGL......NTNTSQHKVRELFN.....K.YGPI..ERIQMVID... ROC_HUMAN/18-82 VFIGNL.....NTLVVKKSDVEAIFS.....K.YGKI..VGCSVHK.... NONA_DROME/304-369 LYVGNL......TNDITDDELREMFK.....P.YGEI..SEIFSNLD... RU17_DROME/104-175 LFIARI......NYDTSESKLRREFE.....F.YGPI..KKIVLIHD... TIA1_HUMAN/216-281 VYCGGV......TSGLTEQLMRQTFS.....P.FGQI..MEIRVFPD... TIA1_HUMAN/9-78 LYVGNL......SRDVTEALILQLFS.....Q.IGPC..KNCKMIMD... PUB1_YEAST/76-146 LYVGNL......DKAITEDILKQYFQ.....V.GGPI..ANIKIMID... SXL_DROME/213-285 LYVTNL......PRTITDDQLDTIFG.....K.YGSI..VQKNILRD... ELAV_DROME/250-322 LYVSGL......PKTMTQQELEAIFA.....P.FGAI..ITSRILQN... SXL_DROME/127-198 LIVNYL......PQDMTDRELYALFR.....A.IGPI..NTCRIMRD... ELV4_HUMAN/48-119 LIVNYL......PQNMTQEEFRSLFG.....S.IGEI..ESCKLVRD... MSSP_HUMAN/31-102 LYIRGL......PPHTTDQDLVKLCQ.....P.YGKI..VSTKAILD... ELAV_DROME/404-475 IFIYNL......APETEEAALWQLFG.....P.FGAV..QSVKIVKD... SQD_DROME/138-208 IFVGGL......TTEISDEEIKTYFG.....Q.FGNI..VEVEMPLD... ROA1_BOVIN/106-176 IFVGGI......KEDTEEHHLRDYFE.....Q.YGKI..EVIEIMTD... CABA_MOUSE/161-231 IFVGGL......NPEATEEKIREYFG.....Q.FGEI..EAIELPID... SQD_DROME/58-128 LFVGGL......SWETTEKELRDHFG.....K.YGEI..ESINVKTD... RB97_DROME/34-104 LFIGGL......APYTTEENLKLFYG.....Q.WGKV..VDVVVMRD... GR10_BRANA/8-79 CFVGGL......AWATGDAELERTFS.....Q.FGEV..IDSKIIND... CABA_MOUSE/77-147 MFVGGL......SWDTSKKDLKDYFT.....K.FGEV..VDCTIKMD... [Part of this file has been deleted for brevity] ROA1_BOVIN/106-176 NCEV CABA_MOUSE/161-231 KCEI SQD_DROME/58-128 KVDP RB97_DROME/34-104 TVEA GR10_BRANA/8-79 TITV CABA_MOUSE/77-147 VIDP SFPQ_HUMAN/373-443 TTPR NONA_DROME/378-448 ASLR NOP3_YEAST/127-190 PLEV GBP2_YEAST/124-193 KLMV U2AF_SCHPO/312-383 KLHA U2AF_HUMAN/261-332 KLLV NUCL_CHICK/283-352 EIKL MODU_DROME/342-410 EWKL RU2B_HUMAN/9-81 PMRI RU1A_HUMAN/12-84 PMRI PUB1_YEAST/342-407 NLRT PTB_HUMAN/186-253 CCTL EWS_HUMAN/363-442 KLKV ARP2_PLAFA/364-438 YLKV YHH5_YEAST/315-384 TIWV PES4_YEAST/305-374 KLLV YHC4_YEAST/348-415 TMHV PR24_YEAST/212-284 EISV MODU_DROME/422-484 PIFI RNP1_YEAST/37-109 KIVI GBP2_YEAST/351-421 SLQI NOP4_YEAST/292-363 LIGD MEI2_SCHPO/197-265 LLYF IF39_YEAST/79-157 RLFL ROF_HUMAN/113-183 YIEV MODU_DROME/260-326 FITV WHI3_YEAST/540-614 TVSS CPO_DROME/453-526 PQTI RU2B_HUMAN/153-220 AMKI RU1A_HUMAN/210-276 NAMK RU1A_YEAST/229-293 NDVT SFR1_HUMAN/122-186 EGET NOP3_YEAST/202-270 VITV U2AG_HUMAN/67-142 PIHA D111_ARATH/285-364 TVRA PR24_YEAST/43-111 EIIV MODU_DROME/177-246 VLSV SSB1_YEAST/39-114 EIHI RN12_YEAST/200-267 VLHI PTB_HUMAN/61-128 PIYI LA_HUMAN/113-182 DLLI LA_DROME/151-225 ELLR PR24_YEAST/119-190 TLVT IF39_SCHPO/41-124 TFVV // |
# STOCKHOLM 1.0 #=GF ID fn3 #=GF AC PF00041 #=GF DE Fibronectin type III domain #=GF AU Sonnhammer ELL #=GF GA 7.8 -1.0 #=GF TC 7.7 7.7 #=GF TC 7.9 0.1 #=GF AL HMM_simulated_annealing #=GF SE Swissprot_feature_table #=GF TP Domain #=GF BM hmmbuild -F HMM_ls SEED #=GF BM hmmcalibrate --seed 0 HMM_ls #=GF BM hmmbuild -f -F HMM_fs SEED #=GF BM hmmcalibrate --seed 0 HMM_fs #=GF AM globalfirst #=GF RN [1] #=GF RM 90384924 #=GF RT Structural design and molecular evolution of a cytokine #=GF RT receptor superfamily. #=GF RA Bazan JF; #=GF RL PNAS USA 1990;87:6934-6938. #=GF RN [2] #=GF RM 95106303 #=GF RT Tracing the spread of fibronectin type III domains in #=GF RT bacterial glycohydrolases. #=GF RA Little E, Bork P, Doolittle R; #=GF RL J Mol Evol 1994;39:631-643. #=GF RC Definition of fibronectin domains #=GF RN [3] #=GF RM 85284965 #=GF RT Primary structure of human fibronectin: differential #=GF RT splicing may generate at least 10 polypeptides from a #=GF RT single gene. #=GF RA Kornblihtt AR, Umezawa K, Vibe-Pedersen K, Baralle FE; #=GF RL EMBO J. 1985;4:1755-1759. #=GF DR PROSITE; PDOC00214; #=GF DR PRINTS; PR00014; #=GF DR SCOP; 1ttf; sf; #=GF DR SMART; FN3; #=GF DR HOMSTRAD; fn3; #=GF DC The following Pfam-B families contain sequences that according to Prodom #=GF DC are members of this Pfam-A family. #=GF DR PFAMB; PB001437; #=GF DR PFAMB; PB004758; #=GF DR PFAMB; PB007041; #=GF DR PFAMB; PB007646; #=GF DR PFAMB; PB012739; #=GF DR PFAMB; PB016725; #=GF DR PFAMB; PB016744; [Part of this file has been deleted for brevity] FAS2_SCHAM/530-616 RFA.AQNEVGF....GPWS PTPZ_HUMAN/312-401 QIV.AICTNGL...YGKYS NCA1_BOVIN/610-691 YVV.AENQQ.......GKS FAS2_SCHAM/642-735 EVR.ATNAIGN....SVPG TIE2_HUMAN/543-626 RAR..VNTKAQ....GEWS TENA_CHICK/682-767 SLH.IVKNNTR...GPGLS UFO_HUMAN/327-411 CVA.AYTAAGD....GPWS TIE1_HUMAN/545-632 DVQ.LYHCTLL....GPAS 7LES_DROME/1799-1891 WVQ.AHATPTK....SNSS NRG_DROME/717-799 KVV.AINDR.......GES #=GR NRG_DROME/717-799 SS EEE.EEEEE.......EEE #=GR NRG_DROME/717-799 SA 030.10200.......020 NRCA_CHICK/726-810 KVQ.ALNDLGY...APEPS NGCA_CHICK/700-794 RVQ.AVNGAGK....GPEA TIE2_HUMAN/639-724 DIF.AENNIGS....SNPA LAR_DROME/515-598 WLA.ARSQRGE....GATT PTP6_DROME/236-321 RIV.GKNSIGN....GQPT TIE2_HUMAN/444-529 CVQ.LVRRGEG....GEGH TIE1_HUMAN/446-533 RVQLSRPGEGG...EGAWG PTPK_MOUSE/290-376 RVLLTRPGEGG...TGLPG PTPB_HUMAN/1355-1434 SIK.VQSAG.......MTS PTP1_DROME/583-661 QVN.TVSFG.......VES PTP1_DROME/312-394 IVK.TVSGK.......VTS PTP1_DROME/217-301 SVQ.TMSED.......EIS PTP1_DROME/123-205 QAY.TIYDG.......KES PTPB_HUMAN/1261-1344 NVK.TVSGDSW....KTYS PTP1_DROME/864-944 TVV.VRSGTESS..VLRSS PTPB_HUMAN/1173-1250 WVV.THSGD........LS PTPB_HUMAN/1085-1162 VIV.THSGE........LS PTPB_HUMAN/467-543 TVT.SISGD........LK PTPB_HUMAN/995-1074 QIL.TVSGG.......LFS PTPB_HUMAN/731-808 TVT.TKSGQ........YE PTPB_HUMAN/643-725 TIT.TRSGKYE...NHSFS PTPB_HUMAN/554-632 VVT.TVSGG.......ISS PTPB_HUMAN/907-984 MIA.SVSGS........LK PTPB_HUMAN/112-192 AIT.AVSGG.......KRS IL7R_HUMAN/129-221 KVR.SIPDHYFKGFWSEWS FINC_BOVIN/689-768 NVY.EISEE.......GEQ KALM_CHICK/178-271 RVA.AVNVHGT...RGFTA TENA_HUMAN/1529-1608 MVS.GFTQG.......HQT TENA_CHICK/1227-1306 ELY.GVSSG.......RRS TENA_CHICK/1136-1215 YLY.GISHG.......FRT TENA_HUMAN/1255-1335 TLH.GEVRG.......HST TENA_CHICK/1045-1124 TLY.GVIRG.......YRT 7LES_DROVI/1917-1997 RLA.LAYAATP....GAPI PTPB_HUMAN/22-103 KII.SLDEE........RT KALM_CHICK/544-642 EVQ.VLTTGGE....GPAT #=GC SS_cons EEE.EEECCCC....CCCC #=GC SA_cons 221.2123454....3232 #=GC seq_cons pVt.Ahsst.......t.S // |
# STOCKHOLM 1.0 #=GF ID pkinase #=GF AC PF00069 #=GF DE Protein kinase domain #=GF AU Sonnhammer ELL #=GF GA -57.9 -57.9 #=GF TC -58.0 -58.0 #=GF TC -57.7 -57.7 #=GF AL Clustalw #=GF SE Unknown #=GF TP Domain #=GF BM hmmbuild -F HMM_ls SEED #=GF BM hmmcalibrate --seed 0 HMM_ls #=GF BM hmmbuild -f -F HMM_fs SEED #=GF BM hmmcalibrate --seed 0 HMM_fs #=GF AM byscore #=GF RN [1] #=GF RM 92065863 #=GF RT Protein kinase catalytic domain sequence database: #=GF RT identification of conserved features of primary structure #=GF RT and classification of family members. #=GF RA Hanks SK, Quinn AM; #=GF RL Methods Enzymol 1991;200:38-62. #=GF RN [2] #=GF RM 95285959 #=GF RT Protein kinases 6. The eukaryotic protein kinase #=GF RT superfamily: kinase (catalytic) domain structure and #=GF RT classification. #=GF RA Hanks SK, Hunter T; #=GF RL FASEB J 1995;9:576-596. #=GF RN [3] #=GF RM 97172697 #=GF RT The protein kinases of budding yeast: six score and more. #=GF RA Hunter T, Plowman GD; #=GF RL Trends Biochem Sci 1997;22:18-22. #=GF DR PROSITE; PDOC00100; #=GF DR PROSITE; PDOC00212; #=GF DR PROSITE; PDOC00213; #=GF DR PROSITE; PDOC00629; #=GF DR PROSITE_PROFILE; PS50011; #=GF DR PRINTS; PR00109; #=GF DC Protein kinase; unclassified specificity. #=GF DR SMART; STYKc; #=GF DC Serine/Threonine protein kinases, catalytic domain #=GF DR SMART; S_TKc; #=GF DC Tyrosine kinase, catalytic domain #=GF DR SMART; TyrKc; #=GF DR SCOP; 1apm; sf; #=GF DR URL; http://www.sdsc.edu/Kinases/pk_home.html; #=GF DR HOMSTRAD; kinase; [Part of this file has been deleted for brevity] #=GR SAT4_YEAST/316-590 AS ..................... KKL6_YEAST/192-508 TLTRKN.QRWSINEIYESPFV #=GR KKL6_YEAST/192-508 AS ..................... RAN1_SCHPO/18-295 PKTRI.....TLPEL..STLV #=GR RAN1_SCHPO/18-295 AS ..................... TRKA_HUMAN/510-781 PQQRH.....SIKDVHARL.. #=GR TRKA_HUMAN/510-781 AS ..................... KSYK_PIG/364-619 VENRP.....GFVAVELRL.. #=GR KSYK_PIG/364-619 AS ..................... BFR2_HUMAN/367-643 PSQRP.....TFKQLVEDL.. #=GR BFR2_HUMAN/367-643 AS ..................... ABL1_CAEEL/311-562 PSDRP.....RFRDIHFNL.. #=GR ABL1_CAEEL/311-562 AS ..................... 7LES_DROME/2209-2481 PWERP.....SFRRCYNTL.. JAK1_HUMAN/864-1137 PSNRT.....SFQNLIEGF.. #=GR JAK1_HUMAN/864-1137 AS ..................... EGFR_DROME/938-1194 AAMRP.....TFKQLTTVF.. #=GR EGFR_DROME/938-1194 AS ..................... RYK_HUMAN/327-593 PEERP.....KFQQLVQCL.. #=GR RYK_HUMAN/327-593 AS ..................... MET_HUMAN/1078-1337 AEMRP.....SFSELVSRI.. #=GR MET_HUMAN/1078-1337 AS ..................... PHY1_CERPU/1004-1282 PLKRP......SFAVICQKL. #=GR PHY1_CERPU/1004-1282 AS ..................... M3K9_HUMAN/3-262 PHSRP.....SFTNILDQL.. #=GR M3K9_HUMAN/3-262 AS ..................... KYK2_DICDI/108-364 PNDRP.....PFTYIVNKL.. #=GR KYK2_DICDI/108-364 AS ..................... KYK1_DICDI/1289-1559 PDSRP.....TFKQIIVHL.. #=GR KYK1_DICDI/1289-1559 AS ..................... KMIL_AVIMH/82-339 REERP.....LFPQILSSI.. #=GR KMIL_AVIMH/82-339 AS ..................... KPRO_MAIZE/534-812 RSKRP.....TMEHAVQTL.. #=GR KPRO_MAIZE/534-812 AS ..................... AVR1_HUMAN/208-495 PSARL.....TALRIKKTL.. #=GR AVR1_HUMAN/208-495 AS ..................... AVR2_HUMAN/192-479 AEARL.....SAGCVGERI.. #=GR AVR2_HUMAN/192-479 AS ..................... PKN1_MYXXA/59-320 PEDRY....ASIAAFRNALQV #=GR PKN1_MYXXA/59-320 AS ..................... KMOS_CERAE/60-338 AAQRP.....SARPLLVDL.. #=GR KMOS_CERAE/60-338 AS ..................... KR1_PRVKA/53-332 PVRRP.....SADEILNFGMW #=GR KR1_PRVKA/53-332 AS ..................... KR1_HSV11/191-478 GALRP.....SAAELLCLPLF #=GR KR1_HSV11/191-478 AS ..................... JAK1_HUMAN/571-833 PNQRP.....FFRAIMRDI.. HR25_YEAST/9-273 FDEKP......DYLFLARLF. #=GR HR25_YEAST/9-273 AS ..................... #=GC seq_cons PppR......ohppllpc.ah // |
HMMER2.0 [2.3.2] NAME globins50 LENG 143 ALPH Amino RF no CS no MAP yes COM /shared/software/bin/hmmbuild -n globins50 --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F globin.hmm ../../data/hmmnew/globins50.msf NSEQ 50 DATE Tue Jan 12 15:39:00 2010 CKSUM 9858 XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 NULT -4 -8455 NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 HMM A C D E F G H I K L M N P Q R S T V W Y m->m m->i m->d i->m i->i d->m d->d b->m m->e -450 * -1900 1 591 -1587 159 1351 -1874 -201 151 -1600 998 -1591 -693 389 -1272 595 42 -31 27 -693 -1797 -1134 14 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 -450 * 2 -926 -2616 2221 2269 -2845 -1178 -325 -2678 -300 -2596 -1810 220 -1592 939 -974 -671 -939 -2204 -2785 -1925 15 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 3 -638 -1715 -680 497 -2043 -1540 23 -1671 2380 -1641 -840 -222 -1595 437 1040 -564 -523 -1363 2124 -1313 16 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 4 829 -1571 -37 660 -1856 -873 152 -1578 894 -1573 -678 769 -1273 1284 58 224 447 -1175 -1782 -1125 17 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 5 369 -433 -475 286 -974 -1312 -19 -412 664 398 406 1030 -1394 388 -214 -261 85 -166 -1227 -725 18 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 6 -1291 -884 -3696 -3261 -1137 -3425 -2802 2322 -3066 111 19 -3028 -3275 -2855 -3100 -2670 -1269 2738 -2450 -2062 19 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 7 157 -413 -236 316 -1387 -1231 89 -863 1084 -431 -348 910 -1319 635 297 15 704 -483 -1497 -922 20 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 8 770 -1431 -43 459 -1751 -340 78 -1449 440 -1497 -631 866 -1302 825 -51 953 364 -1076 -1750 -1121 21 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 9 420 -186 -2172 -1577 8 -1818 -694 1477 -1281 760 614 -1299 -1867 -1001 -1262 -189 -12 1401 -722 -364 22 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 10 -961 -879 -2277 -1821 1366 -2213 -204 -399 -1500 -130 -39 -1427 -2266 -1186 -1511 -159 -913 -367 4721 1177 23 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 11 -48 -1782 809 844 -2073 1456 8 -1811 315 -1803 -932 180 -1365 921 -218 173 -115 -1399 -2018 -1327 24 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - 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-h : Use -help to get help information instead. -f : Use -strategy option instead. -g : Use -strategy option instead. -s : Use -strategy option instead. -A : Set append: "N" or append: "Y" for "hmmfile" in the ACD file instead. -F : Always set (an existing hmmfile will be overwritten). -amino : Sequence alignment type is specified via the ACD file. -nucleic : Sequence alignment type is specified via the ACD file. -informat : All common alignment formats are supported automatically. -wblosum : Use -weighting option to specify the sequence weighting algorithm. -wgsc : Use -weighting option to specify the sequence weighting algorithm. -wme : Use -weighting option to specify the sequence weighting algorithm. -wnone : Use -weighting option to specify the sequence weighting algorithm. -wpb : Use -weighting option to specify the sequence weighting algorithm. -wvoronoi : Use -weighting option to specify the sequence weighting algorithm. -verbose : Use -verbosity instead.
The following additional options are provided:
-weighting : Sequence weighting algorithm. -n : Use -nhmm instead (-n causes problems for GUI developers)
WWW home: http://hmmer.wustl.edu/ Distribution: ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/
set path=(/usr/local/hmmer/bin/ $path) rehash
Please read the 'Notes' section below for a description of the differences between the original and EMBASSY HMMER, particularly which application command line options are supported.
BLASTDB location of sequence databases to be searched BLASMAT location of substitution matrices HMMERDB location of HMMs
Program name | Description |
---|---|
ehmmalign | Align sequences to an HMM profile |
ehmmcalibrate | Calibrate HMM search statistics |
ehmmconvert | Convert between profile HMM file formats |
ehmmemit | Generate sequences from a profile HMM |
ehmmfetch | Retrieve an HMM from an HMM database |
ehmmindex | Create a binary SSI index for an HMM database |
ehmmpfam | Search one or more sequences against an HMM database |
ehmmsearch | Search a sequence database with a profile HMM |
oalistat | Statistics for multiple alignment files |
ohmmalign | Align sequences with an HMM |
ohmmbuild | Build HMM |
ohmmcalibrate | Calibrate a hidden Markov model |
ohmmconvert | Convert between HMM formats |
ohmmemit | Extract HMM sequences |
ohmmfetch | Extract HMM from a database |
ohmmindex | Index an HMM database |
ohmmpfam | Align single sequence with an HMM |
ohmmsearch | Search sequence database with an HMM |
Although we take every care to ensure that the results of the EMBOSS version are identical to those from the original package, we recommend that you check your inputs give the same results in both versions before publication.
Please report all bugs in the EMBOSS version to the EMBOSS bug team,
not to the original author.
Jon Ison (jison © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
This program is an EMBASSY wrapper to a program written by Sean Eddy as part of his hmmer package.
Please report any bugs to the EMBOSS bug team in the first instance, not to Sean Eddy.